If the site's name is descriptive, and not an "empty vessel" name, then I would expect the description to match the content.
The site name is the first, and often only piece of information a person has when visiting a site initially, and they will make assumptions about the site based on the name of the site.
If a descriptive site name does not match its content, then I think a site is not at it's full potential since they are losing what could potentially be a large part of their user base. The loss could occur because the content is not what the user expects, so they leave, or it could occur because users actually searching for a site like the one you provide are not finding your site, or maybe are seeing it, but are assuming it is something else.
For example, here are my assumptions based on the sample links you gave, and my thoughts as your typical new user to the sites about their naming decisions
My assumption: Google's Reader. I would assume I can either read books here, or read files in some custom format.
Actual definition: Going to the site takes me to a page that tells me the site is actually for tracking your favorite sites and new content posted there
Good/Bad site name? Bad, however they made up for it by the initial page which makes it very clear what the site actually is
My assumption: Place on Google to create and store documents
Actual definition: Matches my assumption (and does more!)
Good/Bad site name? Good
My assumption: Site all about fonts, or a place to obtain fonts
Actual definition: Matches my assumption
Good/Bad site name? Good
My assumption: Stack Exchange's site about programmers
Actual definition: Stack Exchange's site for conceptual software development questions
Good/Bad site name? Bad
In my personal opinion (you may not agree), this is a bad site name because the site does not welcome most questions about programmers, and is for Q&A site about software development. There is a welcome message that tells users the site is for "professional programmers interested in conceptual questions about software development", however that is stating that the site is about a specific type of programmer, not about software development.
academia.stackexchange.com - Stack Exchange's site about academia
My assumption: Stack Exchange's site about academics
Actual definition: Welcome message, FAQ, and questions on front page seem to match my assumption
Good/Bad site name? Good, providing my assumption is correct
So to summarize, the site name should ideally match the content of the site if it wants new users to understand what the site is for and how it is used. If it doesn't match, it can still be redeemed by stating the site's purpose clearly on the initial page for new users.
As you said in your question, once users arrive and understand the site, the site name has no significant meaning beyond having to remember what to type to access the site (determining an appropriate name is a different discussion), however if the purpose is to attract new users, then I think the site name should definitely match the content the site provides.